Hi all!
I have some Illumina 100bp paired fastq that I'm planning to map to a reference genome. There is a long story about how I got these reads; the important point is that I just receive them without any prior information about their quality or preprocessing, so I decided to run fastqc... Most of them look quite good and seem ready to be mapped. But some others presents the following patterns: https://ibb.co/fLLYmQ, https://ibb.co/kEhPt5, https://ibb.co/dtCqY5.
According with a post in sourceforge (https://sourceforge.net/p/bio-bwa/mailman/bio-bwa-help/thread/530E1378.3040008@cam.ac.uk/) and what I have heard from several colleagues, Bwa-mem algorithm is quite good at dealing with low quality reads on its own. But I am not sure to which extent this is true. Can I safely go on and map them or would it be better to if I delete the lanes that look problematic. Also, how would another program like stampy fare in this cases?
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You can use BBMap's FilterByTile tool to get rid of just the reads in the problematic parts of a flowcell. But even without that, the reads should map fine.
BWA MEM is a very good choice for longish reads that contain mismatches. I did an evaluation last year that could be useful for you (http://biorxiv.org/content/early/2016/05/16/053686)